Deep-sea explorers said Saturday they had located the wreck of a World War II Japanese transport ship, the Montevideo Maru, which was torpedoed off the Philippines killing nearly 1,000 Australians aboard.

The ship -- sunk on July 1, 1942, by a US submarine whose crew did not realise it carried prisoners of war -- was found at a depth of more than four kilometres (2.5 miles), said the maritime archaeology group Silentworld Foundation, which organised the mission.

The sinking of the Montevideo Maru was Australia's worst-ever maritime disaster, killing an estimated 979 Australian citizens including at least 850 troops.

Civilians from 13 other countries were also aboard, the foundation said, bringing the total number of prisoners killed to about 1,060.

"At long last, the resting place of the lost souls of the Montevideo Maru has been found," Prime Minister Anthony Albanese said.

"Among the 1,060 prisoners on board were 850 Australian service members -- their lives cut short," he said on social media.

"We hope today's news brings a measure of comfort to loved ones who have kept a long vigil."

After five years of planning, explorers began searching for the wreck on April 6 in the South China Sea northwest of the Philippines' main island of Luzon and made a positive sighting just 12 days later using high-tech equipment including an autonomous underwater vehicle with sonar.

The wreckage will remain undisturbed on the seabed, where it lies at a greater depth than the Titanic, out of respect for the families of those who perished, the foundation said. No artefacts or human remains are to be removed.

- 'Terrible chapter' -

 

"The discovery of the Montevideo Maru closes a terrible chapter in Australian military and maritime history," said John Mullen, director of Silentworld, which conducted the hunt with Dutch deep sea survey firm Fugro along with help from the Australian military.

"Families waited for years for news of their missing loved ones before learning of the tragic outcome of the sinking," Mullen said.

"Some never fully came to accept that their loved ones were among the victims."

Andrea Williams, an Australian whose grandfather and great-uncle were civilian internees who perished on the ship, was part of the mission that found the vessel.

She said it was an "extraordinarily momentous day" for Australians connected with the disaster.

"I could never understand why it was not a more powerful part of our Australian WWII history," Williams said in a statement.

Australia's chief of army, Lieutenant General Simon Stuart, said finding the wreck had ended 81 years of uncertainty for the loved ones of those lost.

"A loss like this reaches down through the decades and reminds us all of the human cost of conflict," he said.